The primary objective of the proposed research is the development of a tandem orthogonal acceleration time-of-flight (TOF) mass spectrometer for high throughput proteomics applications with enhanced MS/MS capabilities. This will be achieved by building a dual tandem instrument capable of operating in two different MS/MS modes. Alongside with traditional collision induced dissociation (CID), this instrument will feature a novel fragmentation technique based on the interaction of peptide ions with a flow of metastable atoms or molecules. This new fragmentation technique will cleave different peptide backbone bonds than CID with less dependence on peptide composition and preserve labile posttranslational modifications. Incorporating both techniques in one high performance Q-TOF mass spectrometer will allow using these instruments for high throughput proteomics applications. Proteomics studies biological processes by the systematic analysis of the proteins expressed in a cell or tissue. It plays an important role in modern life sciences, drug discovery, and clinical applications. We propose a new high throughput technology for increasing the efficiency of protein identification and structure elucidation using tandem mass spectrometry. [unreadable] [unreadable] [unreadable]